新型二氟甲基磷酸类酪氨酸蛋白磷酸酯酶1B抑制剂的分子动力学模拟和结合自由能计算（英文）

通过分子对接建立了一系列含二氟甲基磷酸基团（DFMP）或二氟甲基硫酸基团（DFMS）的抑制剂与酪氨酸蛋白磷酸酯酶1B（PTP1B）的相互作用模式,并通过1ns的分子动力学模拟和molecular mechanics/generalized Born surface area（MM/GBSA）方法计算了其结合自由能.计算获得的结合自由能排序和抑制剂与靶酶间结合能力排序一致;通过基于主方程的自由能计算方法,获得了抑制剂与靶酶残基间相互作用的信息,这些信息显示DFMP/DFMS基团的负电荷中心与PTP1B的221位精氨酸正电荷中心之间的静电相互作用强弱决定了此类抑制剂的活性,进一步的分析还显示位于DFMP/DFMS基团中的氟原子或其他具有适当原子半径的氢键供体原子会增进此类抑制剂与PTP1B活性位点的结合能力.     

新型二氟甲基磷酸类酪氨酸蛋白磷酸酯酶1B抑制剂的分子动力学模拟和结合自由能计算

通过分子对接建立了一系列含二氟甲基磷酸基团(DFMP)或二氟甲基硫酸基团(DFMS)的抑制剂与酪氨酸蛋白磷酸酯酶1B(PTP1B)的相互作用模式, 并通过1 ns的分子动力学模拟和molecular mechanics/generalized Born surface area (MM/GBSA)方法计算了其结合自由能. 计算获得的结合自由能排序和抑制剂与靶酶间结合能力排序一致; 通过基于主方程的自由能计算方法, 获得了抑制剂与靶酶残基间相互作用的信息, 这些信息显示DFMP/DFMS基团的负电荷中心与PTP1B的221位精氨酸正电荷中心之间的静电相互作用强弱决定了此类抑制剂的活性, 进一步的分析还显示位于DFMP/DFMS基团中的氟原子或其他具有适当原子半径的氢键供体原子会增进此类抑制剂与PTP1B活性位点的结合能力.     

Hydroxamate类抑制剂与MMP-3的结合自由能的计算

用自由能微扰方法(FEP)计算了两种hydroxamate类的抑制剂和MMP-3的相对结合自由能。在计算中,对于催化区的锌离子与其共价结合的配体(包括抑制和组氨酸)采用了键合的模型,抑制剂和周围配体的部分电荷的计算采用两步静电势收敛方法。自由能计算采用了慢增长(Slowgrowth)和固定窗口增长(Fixedwidthwindowgrowth)两种方法,并且在每次计算中都采用了双向采样(Double-widesampling)的策略。两种方法计算得到的相对结合自由能都能和实验值很好的符合。同时从动力学模拟的得到的分子轨迹得到了抑制剂和受体之间相互作用模式,抑制剂的P1部分可以和受体的S1'口袋形成很强范德华和疏水相互作用,P1上的苯环可以和Tyr223上的苯环形成较好的π键堆积相互作用。     

266 nm激光光解C2H5SSC2H5产物的激光诱导荧光光谱

有机硫化物是大气主要污染物之一,其在大气中的光解产物还将造成二次污染,除了存在于有机硫化物中, S―S键还存在于胱氨酸等蛋白质中, S―S键的形成和断裂决定该类蛋白质的活性.本工作中,我们研究了用实验室常见的Nd:YAG激光器的四倍频266 nm激光光解C₂H₅SSC₂H₅过程,通过激光诱导荧光(LIF)光谱方法检测乙硫自由基C₂H₅S等光解产物.实验表明266 nm激光主要光解C₂H₅SSC₂H₅的S―S键产生C₂H₅S自由基.本文应用密度泛函理论的Becke3-Lee-Yang-Parr泛函(B3LYP方法)得到C₂H₅SSC₂H₅的S―S键、C―S键和C―C键的解离势能曲线,可知在266 nm光解条件下, C₂H₅SSC₂H₅在基态能够发生S―S键、C―S键解离, C―C键不发生解离.本文采用全活化空间自洽场(CASSCF)方法优化得到态和态的C₂H₅S自由基结构及其跃迁的绝热激发能,以辅助解析实验检测的C₂H₅S自由基的LIF光谱.实验结合理论计算最终得出,本实验266 nm光解条件下, C₂H₅SSC₂H₅主要发生S―S键解离,不排除少量分子发生C―S键解离的可能性.     

凝血因子Xa的S4口袋部分关键残基对利伐沙班结合的不同作用机制

通过生物信息学对比、 分子动力学模拟和结合自由能计算分析了利伐沙班与凝血因子Xa的S4口袋部分关键残基之间动态相互作用的细节. 结果表明, 利伐沙班与凝血因子Xa结合不稳定是由S4口袋关键残基突变对疏水盒子完整性的破坏所致. 其中Trp215侧链的疏水作用对抑制剂结合的作用较大, 但对整体结构的影响短时间内较小. Tyr99虽然在结合自由能中贡献较小, 但其突变可能导致99 loop所在结构域的整体构象变化, 从而对于抑制剂或底物的结合特异性产生影响. S4口袋关键残基的不同作用在凝血因子Xa直接抑制剂的药物设计及其拮抗剂的开发中应予以充分考虑.     

用分子模拟方法研究HIV-1整合酶与咖啡酰基类抑制剂的相互作用

用分子对接和分子动力学(MD)模拟方法研究了一类咖啡酰基和没食子酰基类HIV-1整合酶抑制剂与整合酶之间的相互作用模式, 结果表明该类抑制剂分子上的两个侧链基团(咖啡酰基或没食子酰基)与整合酶的DDE基序之间的相互作用对抑制整合酶活性起到关键作用. 当侧链基团为没食子酰基时, 可以提高该类抑制剂与整合酶的结合能力. 采用线性相互作用能方法(LIE)计算了该类抑制剂与整合酶之间的结合自由能, 预测值与实验值相吻合, 均方根偏差RMSD为1.39 kJ•mol^-1, 以上结果可为基于结构的HIV-1整合酶抑制剂设计提供有用的信息.     

评估石杉碱甲杂合体衍生物作为AD症药物活性顺序的简单方法

为了合理化设计、指导具有高活性、低毒性的石杉碱甲杂合体(Huprine X)衍生物的合成, 建立了一个计算结合自由能的新方案, 以实现对该类衍生物活性排列顺序的预测. 该结合自由能由三部分组成: 抑制剂和靶酶的相互作用能; 活性位点残基在结合前后的构象绝对自由能的变化; 抑制剂从稳定构象变为活性构象的自由能增加值. 通过计算已合成的14个杂合体衍生物的结合自由能, 结果显示理论值和实验测定的生物活性值有很好的等级相关性, 其斯皮尔曼相关系数为0.85, 证明了该方法的可行性.     

EGFR和4-苯胺喹唑啉类抑制剂之间相互作用模式的研究

采用分子动力学和MM/PBSA相结合的方法预测了表皮生长因子受体和4-苯胺喹 啉类抑制剂的相互作用模式。在分子动力学采样的基础上,采用MM/PBSA的方法分 别预测了四种可能结合模式下表皮生长因子受体和4-苯胺喹唑啉类抑制剂间的结合 自由能。在MM/PBSA计算中,受体和抑制剂之间的非键相互作用能采用分子力学 (MM)的方法得到;溶剂效应中极性部分对自由能的贡献通过解Possion- Boltzmanne (PB)方程的方法得到;溶液效应中非极性部分对自由能的贡献则通过 分子表面积计算(SA)的方法得到。计算表明,在四种结合模式下,表皮生长因子受 体和4-苯胺喹唑啉类抑制剂之间的结合自由能有较大的差别。在最佳的相互作用模 式中,抑制剂的苯胺部分位于活性口袋的底部,能够与受体残基的非极性侧链产生 很强的范德华和疏水相互作用。抑制剂喹唑啉环上的N(1)原子能够和Met-769上的 NH形成稳定的氢键,而抑制剂上的N(3)原子则和周围的一个水分子形成氢键。同时 ,抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏 水相互作用。最佳结合模式能够很好地解释已有抑制剂结构和活性间的关系。     

基于分子对接和自由能计算的高活性苯并噻唑类ROCK抑制剂的设计、合成和生物学评价

以3个已报道的苯并噻唑类Rho关联含卷曲螺旋蛋白激酶(ROCK)抑制剂(化合物1~3)为研究对象,经分子动力学模拟获得其在ROCK2蛋白结合口袋中的稳定结合构象,通过分子对接结果从氨基酸角度初步揭示了此类抑制剂的结构-活性关系(SAR);然后,对这3个抑制剂进行MM/GBSA结合自由能(ΔG_(bind))研究,结合自由能计算可知ΔG_(bind)与化合物活性之间具有良好的相关性,且范德华作用能(ΔG_(VDW))对ΔG_(bind)的贡献最大.通过自由能分解获得了对于高活性抑制剂具有重要影响的关键残基.最后,根据分子对接和自由能研究结果设计并合成了3类新型苯并噻唑类似物(D1~D10).生物学评价结果表明,这10个化合物分别具有11~288 nmol/L(ROCK1)和2~105 nmol/L(ROCK2)的抑制活性.其中,化合物D3~D5在人肝微粒体代谢研究中展现出比已报道化合物更高的代谢稳定性.本研究不仅为高活性ROCK抑制剂的设计提供了理论指导,也为ROCK的应用研究提供了一系列结构新颖的高活性抑制剂.     

官能化聚四氢呋喃-b-聚异丁烯-b-聚四氢呋喃三嵌段共聚物的合成与性能

采用2-氯-2,4,4-三甲基戊烷或对二枯基氯为引发剂和TiCl4或FeCl3为共引发剂,引发异丁烯(IB)可控/活性正离子聚合与官能端基转化,设计合成不同分子量及窄分子量分布的端基官能化聚异丁烯,如双端烯丙基溴官能化聚异丁烯(Br-PIB-Br)或双端烯丙基胺官能化聚异丁烯(H2N-PIB-NH2).采用烯丙基溴/高氯酸银体系引发四氢呋喃(THF)开环聚合,合成聚四氢呋喃活性链(PTHF+).进一步通过将IB可控/活性正离子聚合与THF可控/活性正离子开环聚合2种方法相结合,设计合成2种新型官能化聚四氢呋喃-b-聚异丁烯-b-聚四氢呋喃(PTHF-b-PIB-b-PTHF)三嵌段共聚物:(1)以上述Br-PIB-Br为大分子引发剂,在AgClO4作用下引发THF活性正离子开环聚合,采用水终止活性链端,设计合成双端为羟基的HO-PTHF-b-PIB-b-PTHF-OH三嵌段共聚物(简称:FIBF-OH);(2)以上述合成的PTHF+活性链与H2NPIB-NH2链端胺基发生高效亲核取代反应,设计合成中间链段连接点含―NH―官能基团的PTHF-b-HNPIB-NH-b-PTHF三嵌段共聚物(简称:FIBF-NH).在上述三嵌段共聚物中,极性PTHF链段与非极性PIB链段的热力学不相容,导致其呈现明显的微相分离,且微观形态与共聚组成相关.PTHF均聚物易结晶,在上述共聚物中由于PTHF链段单端受限致其结晶性减弱.三嵌段共聚物分子链的中间连接点含―NH―官能基团,具有更强的氢键作用,促进PTHF链段重排并结晶,易形成更紧密的超分子网络结构,导致即使在PTHF链段相对分子量为0.7 kg·mol^-1时仍具有较强的结晶性,且结晶熔融温度明显提高.此外,由于FIBF-NH中形成超分子网络结构,使材料具有优异的自修复性能,材料表面的切痕在常温下10 min后可以完全自愈合.本文设计合成的新型官能化PTHF-b-PIB-b-PTHF三嵌段共聚物兼具有PTHF与PIB的优良性能,在生物医用、智能修复等功能材料领域具有潜在的应用前景.     

The effect of heteroatom substitution of sulfur for selenium in glucosidase inhibitors on intestinal α-glucosidase activities

The synthesis of selenium analogues of de-O-sulfonated ponkoranol, a naturally occurring sulfonium-ion glucosidase inhibitor isolated from Salacia reticulata, and their evaluation as glucosidase inhibitors against two recombinant intestinal enzymes maltase glucoamylase (MGAM) and sucrase isomaltase (SI) are described.     

Recent Progress in the Construction of Natural De-O-Sulfonated Sulfonium Sugars with Antidiabetic Activities

A group of sulfonium salts equipped with a polyhydroxylated side-chain structure have been isolated and identified as potent α-glycosidase inhibitors. Consequently, they have become an attractive target in diverse research disciplines, including organic synthesis, drug discovery, and chemical biology. To this end, the development of practical and effective synthetic strategies, especially for more bioactive de-O-sulfonated sulfonium salts, is a significant research area in organic synthesis. An ideal synthetic methodology should provide easily accessible intermediates with high chemical stability for the key coupling reaction to diastereoselectively construct the sulfonium cation center. This minireview summarizes recently developed strategies applied in the construction of natural de-O-sulfonated sulfonium sugars: 1) acid-catalyzed de-O-sulfonation of sulfonium sulfate inner salts, 2) a coupling reaction between side-chain fragments containing leaving groups and a thiosugar, 3) a coupling reaction between side-chain fragments containing epoxide structures and a thiosugar, and 4) a two-step sequential S_N2 nucleophilic substitution between side-chain fragments containing thiol groups and a diiodide derivative.     

Synthesis of sulfonium sulfate analogues of disaccharides and their conversion to chain-extended homologues of salacinol: new glycosidase inhibitors

Four chain extended homologues of salacinol, a naturally occurring glycosidase inhibitor, were prepared for evaluation as inhibitors of glucosidase enzymes involved in the breakdown of carbohydrates. The syntheses involved the reactions of 1,4-anhydro-2,3,5-tri-O-benzyl-4-thio-D-arabinitol with cyclic sulfate derivatives of different monosaccharides. Debenzylation of the products afforded the novel sulfonium sulfate derivatives of D-glucose, D-galactose, D-arabinose, and D-xylose that are of interest in their own right as glycosidase inhibitors. Reduction to the corresponding alditols then afforded the homologues of salacinol containing polyhydroxylated, acyclic chains of 5- and 6-carbons, differing in stereochemistry at the stereogenic centers. Three of the chain-extended homologues inhibited recombinant human maltase glucoamylase, one of the key intestinal enzymes involved in the breakdown of glucose oligosaccharides in the small intestine, with Ki values in the low micromolar range, of approximately the same magnitude as salacinol, thus providing lead candidates for the treatment of Type 2 diabetes.     

Practical Route to Neokotalanol and Its Natural Analogues: Sulfonium Sugars with Antidiabetic Activities

An efficient and divergent approach toward the synthesis of all four de‐O‐sulfonated sulfonium type α‐glucosidase inhibitors, originally isolated from plants of genus Salacia, is reported for the first time. The key strategy features a coupling reaction between thiol derivatives and a diiodide counterpart. The newly designed thiol coupling partner presents high chemical stability, while the diiodide partner could be easily obtained with increased overall yields compared with conventional routes. The intermolecular nucleophilic substitution reaction followed by a diastereoselective intramolecular cyclization provided the target five‐member sulfonium salt structure, which was connected in an α‐orientation to a polyhydroxylated side‐chain moiety.     

Configuration Flipping in Distal Pocket of Multidrug Transporter MexB Impacts the Efflux Inhibitory Mechanism

MexAB-OprM efflux pumps, found in Pseudomonas aeruginosa, play a major role in drug resistance by extruding out drugs and antibiotic molecules from cells. Inhibitors are used to cease the potency of the efflux pumps. In this study, in-silico models are used to investigate the nature of the binding pocket of the MexAB-OprM efflux pump. First, we have performed classical molecular dynamics (MD) simulations to shed light on different aspects of protein–inhibitor interaction in the binding pocket of the pump. Using classical MD simulations, quantum mechanics/molecular mechanics (QM/MM), and various types of analyses, it is found that D13-9001 has a higher binding affinity towards the binding pocket compared to D1 and D2; the results are in sync with the experimental dat. Two stable configurations of D13-9001 are discovered inside the distal pocket which could be one of the primary reasons for the greater efficacy of D13-9001. The free energy barrier upon changing one state to another is calculated by employing umbrella sampling method. Finally, F178 is mutated to have the complete picture as it contributes significantly to the binding energy irrespective of the three inhibitors. Our results may help to design a new generation of inhibitors for such an efflux pump.     

HIV-1整合酶与芳香二酮酸类抑制剂相互作用的分子模拟研究

用分子对接方法研究了一系列芳香二酮酸类抑制剂与HIV-1整合酶的识别及相互作用. 结果表明, 抑制剂结合到整合酶Asp64～Leu68, Thr115～Phe121, Gln148～Lys159和Mg2＋所构成的口袋区, 抑制机理与5CITEP相似. 采用分子动力学模拟和MM/PBSA方法计算了芳香二酮酸类抑制剂与整合酶之间的结合自由能, 计算结果与实验值相吻合, 平均绝对偏差为3.6 kJ/mol, 体系范德华相互作用和溶剂化效应的非极性项是利于形成复合物的主要因素. 相关性分析结果表明, 结合自由能值与疏水相互作用有较强的线性相关(R＝0.61), 基于此, 用多元线性回归方法给出了一个能较强预测芳香二酮酸类抑制剂与HIV-1整合酶的结合自由能预测模型, 为后续基于抑制剂结构的抗HIV-1药物分子设计提供指导.     

Probing molecular mechanism of inhibitor bindings to bromodomain-containing protein 4 based on molecular dynamics simulations and principal component analysis

ABSTRACT

It is well known that bromodomain-containing protein 4 (BRD4) has been thought as a promising target utilized for treating various human diseases, such as inflammatory disorders, malignant tumours, acute myelogenous leukaemia (AML), bone diseases, etc. For this study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were integrated together to uncover binding modes of inhibitors 8P9, 8PU, and 8PX to BRD4(1). The results obtained from binding free energy calculations show that van der Waals interactions act as the main regulator in bindings of inhibitors to BRD4(1). The information stemming from PCA reveals that inhibitor associations extremely affect conformational changes, internal dynamics, and movement patterns of BRD4(1). Residue-based free energy decomposition method was wielded to unveil contributions of independent residues to inhibitor bindings and the data signify that hydrogen bonding interactions and hydrophobic interactions are decisive factors affecting bindings of inhibitors to BRD4(1). Meanwhile, eight residues Trp81, Pro82, Val87, Leu92, Leu94, Cys136, Asn140, and Ile146 are recognized as the common hot interaction spots of three inhibitors with BRD4(1). The results from this work are expected to provide a meaningfully theoretical guidance for design and development of effective inhibitors inhibiting of the activity of BRD4.     

Computational Analysis of Triazole-Based Kojic Acid Analogs as Tyrosinase Inhibitors by Molecular Dynamics and Free Energy Calculations

Molecular docking, molecular dynamics (MD) simulations and the linear interaction energy (LIE) method were used here to predict binding modes and free energy for a set of 1,2,3-triazole-based KA analogs as potent inhibitors of Tyrosinase (TYR), a key metalloenzyme of the melanogenesis process. Initially, molecular docking calculations satisfactorily predicted the binding mode of evaluated KA analogs, where the KA part overlays the crystal conformation of the KA inhibitor into the catalytic site of TYR. The MD simulations were followed by the LIE method, which reproduced the experimental binding free energies for KA analogs with an r² equal to 0.97, suggesting the robustness of our theoretical model. Moreover, the van der Waals contributions performed by some residues such as Phe197, Pro201, Arg209, Met215 and Val218 are responsible for the binding recognition of 1,2,3-triazole-based KA analogs in TYR catalytic site. Finally, our calculations provide suitable validation of the combination of molecular docking, MD, and LIE approaches as a powerful tool in the structure-based drug design of new and potent TYR inhibitors.